4D5D

Crystal structure of CymA from Klebsiella oxytoca

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.902 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Outer-membrane translocation of bulky small molecules by passive diffusion.

van den Berg, B., Prathyusha Bhamidimarri, S., Dahyabhai Prajapati, J., Kleinekathofer, U., Winterhalter, M.

(2015) Proc. Natl. Acad. Sci. U.S.A. 112: E2991-E2999

  • DOI: 10.1073/pnas.1424835112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The outer membrane (OM) of gram-negative bacteria forms a protective layer around the cell that serves as a permeability barrier to prevent unrestricted access of noxious substances. The permeability barrier of the OM results partly from the limited ...

    The outer membrane (OM) of gram-negative bacteria forms a protective layer around the cell that serves as a permeability barrier to prevent unrestricted access of noxious substances. The permeability barrier of the OM results partly from the limited pore diameters of OM diffusion channels. As a consequence, there is an "OM size-exclusion limit," and the uptake of bulky molecules with molecular masses of more than ∼ 600 Da is thought to be mediated by TonB-dependent, active transporters. Intriguingly, the OM protein CymA from Klebsiella oxytoca does not depend on TonB but nevertheless mediates efficient OM passage of cyclodextrins with diameters of up to ∼ 15 Å. Here we show, by using X-ray crystallography, molecular dynamics simulations, and single-channel electrophysiology, that CymA forms a monomeric 14-stranded β-barrel with a large pore that is occluded on the periplasmic side by the N-terminal 15 residues of the protein. Representing a previously unidentified paradigm in OM transport, CymA mediates the passive diffusion of bulky molecules via an elegant transport mechanism in which a mobile element formed by the N terminus acts as a ligand-expelled gate to preserve the permeability barrier of the OM.

    Organizational Affiliation: 

    Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom; bert.van-den-berg@ncl.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYMA
A, B
339Klebsiella oxytocaMutation(s): 0 
Gene Names: cymA
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL		Sub Group: 
Beta-Barrel Membrane Proteins: Porins and Relatives		Protein: 
CymA monomeric outer membrane protein (NHis-SeMet)
Find proteins for Q48391 (Klebsiella oxytoca)
Go to UniProtKB:  Q48391
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C8E
Query on C8E
Download SDF File 
Download CCD File 
A, B
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
 Ligand Interaction
BCD
Query on BCD
Download SDF File 
Download CCD File 
A, B
BETA-CYCLODEXTRIN
CYCLO-HEPTA-AMYLOSE
C42 H70 O35
WHGYBXFWUBPSRW-FOUAGVGXSA-N
 Ligand Interaction
ACX
Query on ACX
Download SDF File 
Download CCD File 
A, B
ALPHA-CYCLODEXTRIN (CYCLOHEXA-AMYLOSE)
C36 H60 O30
HFHDHCJBZVLPGP-RWMJIURBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.902 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 140.160α = 90.00
b = 77.991β = 90.00
c = 109.927γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-06-10
    Type: Source and taxonomy
  • Version 1.2: 2015-06-24
    Type: Database references
  • Version 1.3: 2018-02-21
    Type: Advisory, Database references, Structure summary